Before when all was OK, was App Server running on a separate system distinct from DB Server?
How many physical systems are now running App server software?
To which system were the two new VM installed?

>only these two new VM are running and
>they are the same as other 1 App
if they really were 100% identical to first Server, then results would be the same & no timeouts.
ipso facto, SOMETHING is different!
>APP servers : OS: 2003 Server ORACLE 9i
this is certainly a nice ancient & unsupported combination of hardware & software